Lyoko In Chaos
by HyperSonic02
Summary: A Sonic/Lyoko crossover. Something goes awry when Sonic uses Chaos Control, and meets up with the Lyoko gang. But there are new forces of evil combining their power, will it be too much? No flaming. Don't like? Don't read. Constructive criticism? Fine.
1. The Beginning

A/N: Hey all, here's my first story I've ever written. A lot of you somewhat older members may be wondering why this looks like a case of copyright infringement from code:lyokomaster's old fanfic, titled "Lyoko In Chaos: A New Ally, A New Enemy." Well, don't worry about that too much. I got permission from him to re-write it. He's a nice guy. And that's 'cause he's me! Just thought I'd clear that up. My previous version of the story was never finished due to my young mind drying up on ideas. Well, I'm back, and I'm throwing everything except the basic outline of the old story out the window, and building it back up from scratch. So, under the new alias of HyperSonic02, I present to you a rewrite of my first story, Lyoko In Chaos.

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A loud alarm sounded over the entire island. Several red and orange robots hurried into formation, lances at the ready. Dead silence settled over the area as the ERUs came to a halt, save for the sound of a single engine rumbling in the distance. As dusk settled in, a small plane could be seen over the ocean, making its way over the horizon.

"There it is, Sonic! That's Eggman's base!" Tails pointed at the enormous tower on the island before them. Sonic looked down from the wing he was standing on at his long time friend in the pilot seat, and chuckled.

"Well, looks like the party's about to begin," said Sonic, looking up to the other form on the wing, seeing the serious visage on the echidna's face, save for the fire in his eyes whenever a fight is about to start. "Right, Knuckles?" He looked over, a more angry look on his face.

"Just land this thing so I trash this base for good! This is the last time he's ever going to trick me again!" He snorted, looking back at the base. Sonic just shrugged.

"We've heard that before. Good going, getting him the Chaos Emerald."

"Guys, stop! This is no time for fighting!" Tails practically shouted. "We're almost there!" The plane started to descend, both Sonic and Knuckles ready to jump into the action. As soon as the plane went over the beach, they jumped out, landing on their respective targets and starting to either fight or dash their way through the small army of ERUs and towards the base. Tails' flew over the action, circling around and shooting his blasters into the mass of robots, taking several of them out with each pass. Soon, as he approached Sonic, he held out a ring, shouting out.

"Sonic, catch!" He threw it out to him just as Sonic jumped, catching it and starting to glow with energy. He curled up into his signature spin dash ball and started barreling through all the robots in his path.

A few minutes of fighting ensued, and most of the robots were in complete disarray. Sonic met up with Knuckles and Tails, who had transformed his plane into his own walking robot, the Cyclone.

"Sonic, we'll take care of things out here, go stop Eggman!" Sonic nodded and grinned, spinning at great speeds before barreling into the base, a visible hole in the wall as the ERUs started to go after him. They didn't get far as a large robot and one angry echidna stood in their way.

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Inside the Base

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Eggman was spastically running from one end to the other in his control room, fearing the worst as soon as the alarm sounded. He frantically put in computer commands into a huge machine in the core of his room. He laughed aloud as he neared completion, holding his most recently acquired Chaos Emerald in his hand.

"Finally, after all these preparations, my Wave Pulse Generator is complete! Let's see how those coastal cities will like it when a giant wall of water crashes down on top of their heads! Now just to insert this final Emera--"

An explosion cut him off as a spiky form stood in the recently-made opening in the control room. Sonic quickly leaped up and bounced off the wall, snatching the blue Emerald out of the evil doctor's hand. He looked back and flashed him a toothy grin.

"Your bases aren't getting much better, Eggman." He chuckled again as the evil genius fumed, nonchalantly tossing the Emerald into the air and catching it.

"Gah, Sonic! This is the last time you're going to make a fool out of me!" Eggman jammed his fist on a button, causing multiple silos to open up on one side of the room. Out of each of them came a missile, quickly training in on the hedgehog and accelerating toward him.

"Whoa!" He shouted out as he jumped out of the way, thinking they would run into a wall or some other obstruction. But they all turned to his new location, homing in on him. He frantically jumped across the room, every now and then a missile would hit something and cause a small explosion. He finally stopped and waited near the core of the room, by Eggman's new invention. Eggman shouted out in protest, but Sonic dashed away at the last second, and before the intelligent missiles could turn around, they made contact with the machine and exploded, destroying it.

"NO! My invention!" Eggman stood there, gawking at his ruined machine. Grunting at his apparent loss, he quickly dashed into his Egg-pod vehicle and quickly flew away out of the broken window, which had probably been destroyed by one of the stray missiles. Sonic quickly gathered up the Emeralds and was about to run out the door, but it was blocked off by debris. The base started to rumble, and explosions were frequent. A last resort crossed his mind, and he instinctively held out the stone he had taken earlier, and shouted two simple words: "Chaos Control!"

However, within that split second of the given command, a black vapor poured out of a live wire that was now dangling, and made contact with the Emerald the moment Sonic vanished in a flash of light.

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Outside the Base

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Knuckles and Tails had at last dispatched of the last of the robot army, with the last of them running away to the other side of the island. Knuckles growled and started to give chase. "Come back here you cowards!"

"Knuckles, forget about them! We have to help--"

Tails didn't even have to bother finishing his sentence. The ground shook, and a pillar of light erupted from the top of the tower-like base as a humungous explosion engulfed it. The dust didn't clear for many minutes as they ran to an area safe from falling debris. After it had, they both yelled out "Sonic!" simultaneously and ran over to the rather large crater. Knuckles started pushing and throwing random pieces of debris out of the way, with Tails just sighing as he looked at his screen.

"Forget it Knuckles, he's not here."

"What? But where could he have gone?!"

Tails shrugged. "Maybe he used the Emeralds to get out."

Knuckles crossed his arms and bowed his head down in deep thought. "Then where could he have gone…?"

Tails shook his head, then suddenly ran behind Knuckles, digging into the debris and pulling out the cyan Chaos Emerald. "We could use this to find out! Let's head to my workshop!"

Knuckles punched his fists against one another and jumped back onto the wing of the plane as soon as Tails had changed it back, and they took off.

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Unknown Location

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Sonic grunted as he woke up, finding himself lying on the ground. He shook his head as he kneeled and then stood up, the first thing crossing his mind was the fact that he was only holding one Emerald. He frantically checked himself, only finding the blue Chaos Emerald and his ring.

"Well at least I have these…" He trailed off as he looked around, no longer finding himself on the island.

"Wait a second... Where am I…?"

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A/N: Well, there you have it, my first chapter of a rewrite of a story I never finished. Maybe I will this time! And if you old members are still out there, if you flame me, don't flame me because my writing style changed. It's been 4 years.

Anyway, I'll be working on the next chapter and maybe it'll be ready in a week, tops. I just started getting back into gear with writing, so bear with me. 'Till next time!


	2. The Discovery

A/N: Alright, here's the second chapter. Probably gonna be a bit more wordy than the last one, I didn't realize it was so short! I'll try to stay on top of that. Also, if you read it, please review it, fellow people. I love to know what you think, good or bad. As long criticism (and praise) is thought out and well written, there's probably a better chance of me using your ideas if you care to share any. Anyway, enjoy!

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Unknown Location

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"What a second… Where am I…?"

Sonic turned a whole revolution as he looked around his new surroundings, taking it all in. The only way he could describe the surrounding landscape was as a desert, save for very abnormal features, such as the fact that there were several floating platforms that made up the "floor." He looked ahead of him, seeing a strange, tall, white structure, with a ghostly blue glow surrounding the top. Slowly, he walked over to the edge of the platform. He struggled to keep his balance for a few moments, as physics seemed to act very differently in this strange world. As soon as he reached the end of the platform, he looked down. All he saw was an endless sheet of orange, with data streams randomly floating around in the water… Was it water? He looked around at the distance again.

"There's no one around here for miles, either, I wonder if… huh?" He trailed off as he saw movement in the distance. He narrowed his eyes to try and peer further, finding he couldn't. He backed up a bit, getting a fast running start to jump onto the next platform that he had spied something on. As he ran closer at a "relatively slow" pace, he was able to make out forms. A pink-haired figure was running from 3 green bug-like creatures, which were shooting lasers from their stingers at her. From what he gathered, those bugs would have to be taken care of.

As he got closer, the bugs spotted Sonic in the distance and veered off from the girl they were chasing and started coming straight at him, their lasers firing all the while. Clutching the Crystal Ring, he leaped into the air, his arms and legs snapping together as he spun wildly. He crashed right into one of the creatures, destroying it outright, and the pieces of it faded away. He turned around in midair and landed on top of the second hornet, bringing it down with him. The creature was unable to regain its aerial composure before Sonic did a quick backflip, bringing his foot out to kick the hornet right into the last one. The impact destroyed them both.

He flipped down to the ground, landing on both feet and bending his knees to absorb the impact. Surprisingly, he didn't find as much as one. He flicked the Crystal Ring up into the air and it slid right down his finger, snapping tight around as it shrunk around it.

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Aelita narrowed her eyes in curiosity as the blue form took out the hornets with incredible speed, unlike anything she had seen here on Lyoko. She waited a few long moments after the battle was finished, watching the glinting ring go on the form's gloved finger. She slowly walked up to him, tilting her head, but cautiously keeping her distance as best she could. As she stopped, he turned his head around at her and grinned, looking around at the ground around him for a moment.

"Well, I don't usually play exterminator, but whatever works…" He looked back up at her, and she backed up one step reflexively. She was reassured when he asked, "Are you alright?"

She nodded slowly and came forward a few steps. She leaned forward a bit, examining him. "Are you with Xana?"

The hedgehog looked at her quizzically. "What's Xana?"

Aelita sighed with relief and smiled slightly, moving up a bit closer, mere feet away from this stranger. "Never mind. I'm Aelita, who are you?"

He grinned again and nodded, moving up a bit closer to her and holding out his hand in greeting. "I'm Sonic, Sonic the Hedgehog."

Aelita smiled and took his hand, shaking it for a moment before leaning forward again to examine him further. "How did you get here on Lyoko? Are you one of Jeremy's annex programs?"

Again, Sonic looked at her with a confused look. "Lyoko? Jeremy? Program?"

Aelita was about to continue asking questions when she saw movement off in the distance. About four black spheres were coming towards them, and quickly.

"We should get out of here, I'll explain in one of the towers." Aelita made a motion for him to follow her, and she started to run off. Sonic, still getting used to the physics of this world, managed to outpace her, but not by much. Still, they managed to get to the tower long before the megatanks caught up to them. Aelita held out her hand for Sonic to hold onto, and as soon as he had a grip, they slowly walked through the tower.

When they were in, Sonic shook his head a bit, trying to shake away some dizziness that had come over him when they went through the tower wall. Aelita let go of his hand and she went to the center of the platform they were on. Sonic looked down at the strange pattern of lights on the floor. After thinking for a moment, he realized that this symbol was the same as the symbol on the head plates of the hornets.

After making a futile effort to make a connection, he looked up, seeing Aelita tinkering with what seemed to be a floating computer screen. After moving many windows around and a loading bar filling its way up to 100%, another window showed up and Aelita spoke.

"Jeremy? Jeremy, are you there?"

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Kadic High School: Dorms

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"Jeremy, are you there?"

Jeremy slowly woke up to the familiar voice coming from his dorm computer, sitting up and rubbing his eyes. He looked over at the clock; it was 2:30 on Saturday morning. He walked up to the computer and sat down, rapidly putting in keystrokes and getting a visual of Aelita.

"Hey Aelita, is everything okay? Is Xana attacking?"

"No, Xana has been quiet, save for getting attacked earlier. But Sonic saved me from Xana's monsters." Aelita brought up a visual of her line of sight, and Jeremy could see Sonic in the window. He was astonished.

"Sonic the Hedgehog? Aren't you supposed to be on the other side of the world in Station Square?"

Sonic shrugged, with a look of carefree confusion. "I don't know what's going on, really."

He explained to both Aelita and Jeremy all he knew: the attack on Eggman's base, the Chaos Emeralds, Chaos Control's fundamentals, and how he came to meet Aelita.

"…so she brought me into this tower thing, and now I'm here." Jeremy nodded as he pondered the situation, while Aelita, doing some thinking of her own, looked at both of them.

"Perhaps Xana does have something to do with this… He has been quiet as of late." Sonic shook his head in slight frustration, and looked up.

"Okay, where am I, what's this Xana thing, and what's going on?" He said that a bit more sharply than he anticipated, but he looked into the screen at Jeremy and Aelita, his arms crossed and tapping his foot. The other two seemed a bit taken aback, but they did their best to explain the situation. They explained what Lyoko was, the story behind Xana and his apparent intentions, Aelita's virus, and about the rest of the gang. Sonic nodded, seeming to understand for the most part. 'Boy, this is more confusing than Tails explaining a new gadget of his…' he thought as Jeremy finished up his thesis.

"So, perhaps Xana did have something to do with your being here. Since neither Aelita or I had anything to do with it, and with Xana being the only other intelligent being on Lyoko, it's only logical." Aelita nodded in agreement.

"So what do I do, am I stuck here?" Sonic uncrossed his arms, looking at Jeremy and occasionally glancing at the hundreds of screens surrounding the black walls of the tower.

"No, we should be able to dematerialize you with the program we developed for Aelita originally. But you'll need to get to a way tower."

Aelita nodded again, thinking a bit. "Should we go there now? Or wait?"

"Probably wait, I'll call the others just in case Xana is up to something else in the meantime. Stay put until I get to the factory."

Sonic let out a sigh with a hint of impatient frustration, but nodded along with Aelita as the window closed out. Jeremy got up and dressed quickly, getting his laptop into his backpack and getting out of his dorm. He quickly but quietly went over to Odd's and Ulrich's room, and opened the door silently. Kiwi was sleeping on Odd's bed as usual, waking up as soon as Jeremy stepped in. He started barking at Jeremy, causing Odd and Ulrich to wake up.

"Ugh, Jeremy, it's only 3:30... We can study for the geometry test in the morning…" Ulrich said sleepily and between yawns, before putting his pillow over his head in a vain attempt to go back to sleep.

"We have an issue on Lyoko!"

Ulrich and Odd both shot up. "What, is it a Xana attack?"

Jeremy shook his head. "No, it's unlikely, no towers are activated. But Xana could have caused the issue. Are you coming, or what?"

Odd yawned as he stretched out his arms. "Then what's the problem, Einstein?"

Jeremy sighed and opened his phone, dialing Yumi's number. "Better if you see for yourself. Come on, hurry up!"

The two swung their legs over the bed, shaking off the rest of their sleepiness before quickly getting dressed into their usual attire. As they did, Jeremy sent Yumi a quick call to tell her to do the same and meet them at the factory. The three teenagers quickly ran into the school boiler room down the stairwell, riding through the sewer on their respective rides towards the factory entry point.

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Tails' Workshop

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Tails frustratingly looked around his virtual representation of the globe on his reasonably large computer screen, rotating the planet every direction several times, looking for a tell-tale blip on the screen. The cyan Chaos Emerald glowed in a nearby power cell, seemingly connected to the computer by a series of wires.

"Well? Where is he?" Knuckles leaned against the back wall, his eyes closed in deep thought.

Tails sighed and expanded the view, clicking on a small location pin he had made to quickly take a look at the ARK, in case Sonic had for some reason gone there. No luck. "I don't know. We should be able to find him anywhere on the planet, and in near space. Where else could he have gone?" Knuckles gave him a passive shrug. Just as he turned back around to the computer to do another quick search, his phone on the nearby desk started to ring. He looked at the caller ID and sighed, a tired, annoyed look on his face as he answered.

"Hey, Amy."

"Hey Tails, just calling to see how the mission went, is Sonic there?"

"Oh, uh…" Tails' visage went from annoyed to scared as he hesitatingly replied. "We're looking for him now…"

"WHAT?" Tails held the phone a foot away from his ear as Amy drastically rose her voice.

"He just vanished, we don't know where he is… Amy, are you there?" Tails spoke into the phone as it went dead quiet on the other end. Moments later, he and Knuckles both rose their heads at the metal sliding door, which opened to reveal an angry-looking pink hedgehog with a really, really big hammer.

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Eggman's Main Base

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Eggman grunted and pounded his fist into his chair as he thought about the latest of his long line of defeats. He looked out his control room into the main area of the base, his robots frantically reassembling the rest of the army that had been destroyed. He ran his hand over his face as the scrap metal heap continuously got taller.

"Why, why do I always have to lose to that cursed hedgehog and his annoying little friends!" He pounded his fist down again. "I am Eggman, I'm a genius! He can't always…" He trailed off as his computer screen in front of him started spazzing out. He pounded his fist once again on top of it.

"What is up with this blasted… what the?" He stopped banging when the computer screen suddenly showed a red symbol, looking like a strange cross between an eye and a target. Text started typing itself on the screen.

"DR. IVO ROBOTNIK. I AM XANA. I HAVE CONTEMPLATED THAT YOUR DEVICES AND MECHANICAL PROWESS MAY BE USEFUL TO ME. I AM ALSO AWARE THAT YOU HAVE A RIVALRY WITH SONIC THE HEDGEHOG, WHO I KNOW THE WHEREABOUTS OF. WILL YOU ASSIST? Y/N"

Eggman stared dumbfounded at the machine. A digital, sentient being was communicating him through his computer? He typed back.

"You can help me defeat Sonic?"

"YES. WILL YOU ASSIST? Y/N"

Eggman pondered for a moment and sighed. He didn't know much, but if there was a chance at getting rid of the hedgehog for good, it was worth it. He pressed 'Y.'

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What's happening with Eggman and Xana? How will the gang get Sonic out of Lyoko? How bad is Amy going to hurt Tails and Knuckles? Find out in the next chapter!

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A/N: Yay, it's done! One point I want to address right away is that I know the Xana communicating with Eggman is a little strange, but it's hard to forge some semblance of a personality for something that's never shown any, and technically shouldn't have any. On that note, I think I did rather well. The next one has battle scenes! Oh, the joy of keeping track of life points. Anyway, I'll have it up relatively soon!


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